// assume the spectrum read sequentially
public double GetMonoMass(ISpectrum spectrum)
{
if (spectrum.GetMSnOrder() == 1)
{
List <IPoint> points = new List <IPoint>();
foreach (IPeak pk in spectrum.GetPeaks())
{
points.Add(new PeakPoint(pk));
}
matcher.setData(points);
return(0);
}
ISpectrumMSn spectrumMSn = spectrum as ISpectrumMSn;
double mz = spectrumMSn.GetParentMZ();
double monoMass = mz;
// search isotopic point on full MS spectrum
int charge = spectrumMSn.GetParentCharge();
int isotopic = 0;
while (isotopic < maxIsotopic)
{
double target = mz - Proton / charge * (isotopic + 1);
if (!matcher.Found(new GeneralPoint(target)))
{
break;
}
isotopic++;
}
// get max intensity peak
if (isotopic == 0)
{
return(monoMass);
}
double isoMZ = mz - Proton / charge * isotopic;
List <IPoint> matched = matcher.Search(new GeneralPoint(isoMZ));
return(matched.OrderBy(x => Math.Abs((x as PeakPoint).MZ - isoMZ)).First().GetValue());
}
public void Run()
{
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
specRunner.Run(@"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\ZC_20171218_H95_R1.raw");
ISpectrum spectrum = specRunner.GetSpectrum(7859);
ISpectrumMSn msnSpectrum = specRunner.GetSpectrum(7861) as ISpectrumMSn;
IMonoMassSpectrumRun monoRunner = new BinSearchMonoMassSpectrumRun();
monoRunner.SetMS1Spectrum(spectrum);
monoRunner.Run(msnSpectrum);
Console.WriteLine(monoRunner.GetIsotopic());
//ISpectrumProcessing processor = new GeneralPeakPickingSpectrumProcessing();
////processor.Process(spectrum);
//int charge = 4;
//double Hydrogen = 1.0078;
//int indx = PreciseMatch(1198.48413085938, Find(1198.48413085938, peaks, 10), peaks);
//double ppm = UtilMass.Instance.CalcPPM(peaks[indx].GetMZ(), 1198.48413085938);
//Console.WriteLine(ppm);
//Console.WriteLine(peaks[indx].GetIntensity());
//double mz = peaks[indx].GetMZ();
//Console.WriteLine(peaks[FindMassPeak(mz - Hydrogen/charge, peaks, 5)].GetMZ());
//Console.WriteLine(peaks[FindMassPeak(mz - Hydrogen/charge * 2, peaks, 5)].GetMZ());
//Console.WriteLine(peaks[FindMassPeak(mz - Hydrogen/charge * 3, peaks, 5)].GetMZ());
Console.Read();
}
public override void Run(ISpectrumMSn spectrum)
{
if (msSpectrum == null)
{
monoPeak = null;
monoMass = spectrum.GetParentMZ();
return;
}
List <IPeak> peaks = msSpectrum.GetPeaks();
double mz = spectrum.GetParentMZ();
int charge = spectrum.GetParentCharge();
double Proton = UtilMass.Hydrogen;
isotopics = 0;
int index = FindMassPeak(mz, peaks, tol);
while (isotopics < 10)
{
int matchIndex = FindMassPeak(mz - Proton / charge * (isotopics + 1), peaks, tol);
if (matchIndex > 0)
{
isotopics++;
index = matchIndex;
}
else
{
break;
}
}
if (index > 0)
{
monoPeak = peaks[index];
monoMass = monoPeak.GetMZ();
}
else
{
monoPeak = null;
monoMass = mz;
}
}
public void Run()
{
var watch = new System.Diagnostics.Stopwatch();
watch.Start();
FastaSearchRunPeptides pepRunner = new FastaSearchRunPeptides();
pepRunner.SetPeptideCreator(new NGlycosylationPeptideCreator(new GeneralPeptideCreator()));
List <IPeptide> peptides = pepRunner.Run(@"C:\Users\iruiz\Downloads\ms_fasta.fasta");
//List<IPeptide> peptides = pepRunner.Run(@"C:\Users\rz20\Downloads\ms_fasta.fasta");
Console.WriteLine(peptides.Count);
IAccumulatedMSNGlycanCreator glyRunner = new AccumulatedMSBruteForceNGlycanCreator();
List <IAccumulatedGlycanMassProxy> glycans = glyRunner.GenerateSpecific();
//IGlycanGenerator glyRunner = new SimpleGlycanGenerator();
//List<IGlycan> glycans = glyRunner.Generate();
ThermoRawSearchRunSpectrum specRunner = new ThermoRawSearchRunSpectrum();
specRunner.Run(@"C:\Users\iruiz\Downloads\ZC_20171218_H95_R1.raw");
//specRunner.Run(@"C:\Users\rz20\Downloads\ZC_20171218_H95_R1.raw");
ISpectrumMSn spectrum = specRunner.GetSpectrum(7861) as ISpectrumMSn;
List <IGlycan> glycanSet = new List <IGlycan>();
glycanSet.AddRange(glycans);
//IAccumulatedPrecursorMatcher matcher = new AccumulatedNGlycoPeptidePrecursorMatcher(peptides, glycanSet, 20);
//List<IAccumulatedGlycoPeptideMassProxy> glycoPeptides = matcher.Match(spectrum);
IPrecursorMatcher matcher = new GlycoPeptidePrecursorMatcher(peptides, glycanSet, 20);
List <IGlycoPeptide> glycoPeptides = matcher.Match(spectrum);
//int last = specRunner.GetLastScan();
//for (int i = 0; i <= last; i++)
//{
// specRunner.GetSpectrum(i);
//}
//specRunner.Run(@"C:\Users\iruiz\Downloads\2.raw");
//last = specRunner.GetLastScan();
//for (int i = 0; i <= last; i++)
//{
// specRunner.GetSpectrum(i);
//}
//specRunner.Exit();
watch.Stop();
Console.WriteLine(glycans.Count);
Console.WriteLine(glycoPeptides.Count);
foreach (IGlycoPeptide gly in glycoPeptides)
{
Console.WriteLine(gly.GetPeptide().GetSequence());
Console.WriteLine(gly.GetGlycan().GetName());
}
Console.WriteLine($"Execution Time: {watch.ElapsedMilliseconds} ms");
Console.Read();
}
public abstract void Run(ISpectrumMSn spectrum);
